Integrative analysis of metagenomics and metabolomics reveals rhizospheric regulatory strategies for soybean adaptation to gradient phosphorus stress

Abstract

Background and aims

Soybean is sensitive to phosphorus (P) supply, but the rhizosphere ecological mechanisms underlying its low-P tolerance, particularly the synergistic regulatory network between microorganisms and metabolites, are not well understood. This study aimed to integrate metagenomics and metabolomics to reveal the rhizosphere regulatory strategies of soybean in response to graded low-P stress.

Methods

Three P levels were established (severe deficiency, P0; mild deficiency, P30; sufficiency, P90) using two soybean cultivars (P-efficient AX and P-sensitive NM). The study systematically analyzed their rhizosphere P-cycling microbial communities, functional genes, and metabolites.

Results

Extreme low P (AX0) triggered community reorganization in the AX rhizosphere, specifically enriching Actinobacteria and Acidobacteria, upregulating the polyphosphate degradation genes spoT and ppgK, and downregulating the P transporter genes phnC and phnD. In contrast, under NM30 conditions, the abundance of the polyphosphate degradation gene pap was significantly upregulated, and the relative abundance of Proteobacteria increased. Metabolomics analysis showed that both varieties upregulated tyramine, L-phenylalanine, and trans-cinnamic acid, and downregulated stachyose, choline sulfate, and maltotriose under low-P conditions, while caprylic acid was specifically upregulated only in AX under low P. Correlation analysis indicated that P-cycling microorganisms/genes were significantly correlated with soil available P (AP) and acid phosphatase activity (S-ACP) (p < 0.01), while the rhizosphere metabolite profile was highly correlated with plant P accumulation and biomass (R² > 0.85). Partial Least Squares Path Modeling (PLS-PM) further confirmed that rhizosphere metabolites are a key link between microbial functions and plant P acquisition, with the strongest direct contribution to soil P availability.

Conclusion

P-efficient soybeans cope with low-P stress through an “internal turnover” strategy, activating polyphosphate degradation pathways and secreting specific metabolites such as caprylic acid, which synergistically enriches microbial groups with P transformation potential (e.g., Actinobacteria, Acidobacteria). In contrast, the P-sensitive variety exhibited a weaker “external dependency” mode, recruiting Proteobacteria early and inducing the expression of some degradation genes while suppressing the exudation of carbon metabolites. This study elucidates the rhizosphere microecological mechanisms underlying differences in P efficiency in soybean and provides theoretical support and potential targets for low-P tolerance breeding.

Graphical abstract